Okay, now having had some time to look at the primer and go over my paper list (which has deviated somewhat from the version here), I have a few questions and comments.
First, and perhaps most importantly:
Also, cut Draco. That card is not good.
You lie, sir. If I had a card with nothing but "Suspend 1--0: Put this card in your graveyard. If this card is revealed by the effect of
Yuriko, the Tiger's Shadow, count its CMC as 16," I would play it. It's just too much damage to not be worth running a single dead card, especially with things like
Scroll Rack loops to double up on the triggers. Dealing 80% of your opponents' life in one combat step is fantastic.
Second, and perhaps least importantly, it's ninjUtsu. With a U. 忍術(ninjutsu) means "secret art" or "spy technique" or something along those lines, while 忍実(ninjitsu) would be something like "true secrecy." This point is pedantic, but I lived in Japan and that made my eyes itch.
Next, it looks like our builds differ a bit in strategy. I run a small number of evasive creatures, a massive amount of topdeck manipulation, and several ways of making my ninjas unblockable so that I don't have to rely on evasive 1/1s in the mid game. My deck is also wildly more expensive, due to me apparently having no self control. I will take your different strategy and greater financial discipline into consideration when making recommendations.
As far as little evasive creatures, you seem to have most of the good ones, including a few I've overlooked or neglected to add with new expansions. (Looking at you,
Gingerbrute.) I would say that, if you can justify the cost,
Nether Traitor is an all star in my deck. Haste, Shadow, and built in recursion on a cheap attacker make it perfect in every way for Yuriko. Also, how do you feel about
Amoeboid Changeling,
Mist-Syndicate Naga,
Siren Stormtamer, and
Universal Automaton? The first feels too slow, but I can see the utility and I might give it a shot. I didn't like
Mist-Syndicate Naga because it felt like I always ninjustu'd it in, made a copy, and then both copies did very little.
Siren Stormtamer is often great, but do you find your opponents just wait for you to bounce it out before playing removal, especially given that they probably want to hit your ninjas anyway? Finally, is
Universal Automaton worth it as a 1 CMC
ninja? (Are we supposed to say 1 MV, now?)
For unblockable-ness (unblockability?),
Thassa, God of the Sea is obviously very good. She's also $20. You already have
Aqueous Form, but I also like
Aether Tunnel and
Smoke Shroud for pushing ninjas through when I don't have a ready bounce effect for them. I also like
Whispersilk Cloak, but I understand your reasoning for leaving it out.
Since you mentioned not missing board wipes and liking mass bounce better, two of my favorite mass bounce spells are
Devastation Tide and
Evacuation. If you decide you want to start running wipes, these are great for resetting your opponents' boards while you get some extra combat steps in, not to mention that
Evacuation is instant speed. I also like
Rags // Riches, but mostly because it hits mana dorks and is a good flip for Yuriko.
For topdeck filtering, I was going to recommend
Insidious Dreams, Lim-Dul's Vault, and
Doomsday for the utility/memes, but I just found out they're all over $10 now. So instead,
Bolas's Citadel is pretty damn good at getting low cost spells off the top. The downside is that you have to obey normal timing and can't exceed land per turn limits. Still, more topdeck manipulation is always good for Yuriko, in my experience.
For protection, the only card I can really recommend is
Walker of Secret Ways. She's a
ninja. She bounces ninjas. She's cheap. What's not to love? The fact that it only works on your turn. That part is occasionally annoying. Still, she saves ninjas that people target before damage step.
Last, I would say that
Wound Reflection and
Quietus Spike are great ways to do more damage. The former is a bit expensive mana-wise, but often pays you back by turning one or two triggers into a game winning turn.
Quietus Spike is just nice to stick on an unblockable creature early or on something small later to force your opponents to block a 1/1 instead of a
ninja.
Overall, I really enjoyed seeing your list and I thought it was well-built. I had never considered running
Viscera Seer as a way to instantly move Yuriko around, and
Trickery Charm and
Soothsaying are both so good I'm amazed I've never seen them before. Nice job on the primer. If you want any help making variant budget lists or anything like that, let me know.